[Mne_analysis] Guidance on FreeSurfer integration with MNE {Disarmed}

Alexandre Gramfort alexandre.gramfort at inria.fr
Fri Dec 25 04:23:43 EST 2020
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maybe have a look at


On Tue, Dec 22, 2020 at 12:31 PM Parth Chholak <parthchholak at gmail.com>

>         External Email - Use Caution
> Dear all,
> I don't have individual MRI scans for a MEG study and only have
> digitization points collected via a Polhemus tracker. Hence, I would like
> to use 'fsaverage' as a standard anatomy and transform it for each subject
> using digitised points. All MNE tutorials assume that the complete anatomy
> files would already be prepared using FreeSurfer.
> All I could find on FreeSurfer documentation was to use this command:
> recon-all -i path_to_T1.mgz -subjid subject_name
> In one of the MNE workshops in winter last year, I remember a
> demonstration to do the whole thing by Alex. It involved using the
> FreeSurfer GUI and feeding in the FIF file to provide the channel and
> digitization data. I somehow even managed to repeat the whole process
> myself in the summer but unfortunately didn't document it. And now, I can't
> seem to make that miracle happen again.
> I hope it is a valid question to ask on this forum given the strong
> dependency of MNE on this processing step. Any help or direction would be
> greatly appreciated.
> Kind regards,
> *Parth Chholak*
> Doctoral Candidate
> Centre for Biomedical Technology
> Technical University of Spain
> +34 618689339979278
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